suppressMessages(library(ArchR))
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
options(stringsAsFactors = F)
options(repr.plot.width=11, repr.plot.height=8.5)
##################################
### set Arrow File parameters ####
addArchRThreads(threads = 10)
addArchRGenome("mm10")
Setting default number of Parallel threads to 10. Setting default genome to Mm10.
PROJDIR='../../../data/raw_data/mm10/BICCN_mouse_caudoputamen'
ARCHDIR=file.path(PROJDIR,'ArchR_BICCN_CP')
proj = loadArchRProject(ARCHDIR)
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# plot the confusion matrix of cell types by subjects
cM <- confusionMatrix(paste0(proj$L2cluster), paste0(proj$Sample))
cM <- cM / Matrix::colSums(cM)
p <- pheatmap::pheatmap(
mat = as.matrix(cM),
color = paletteContinuous("whiteBlue"),
border_color = "black")
p
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "L2cluster", embedding = "UMAP")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "RegionName", embedding = "UMAP")
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Sample", embedding = "UMAP")
ggAlignPlots(p1, p2, type = "h")
p1
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f3c4b542a-Date-2021-01-22_Time-09-39-20.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f3c4b542a-Date-2021-01-22_Time-09-39-20.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f625b2283-Date-2021-01-22_Time-09-39-27.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f625b2283-Date-2021-01-22_Time-09-39-27.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f46ece199-Date-2021-01-22_Time-09-39-28.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f46ece199-Date-2021-01-22_Time-09-39-28.log
# Broad MSN marker, mouse 2010300C02Rik == human KIAA1211L
# MSN markers, Ppp1r1b = DARPP-32, Bcl11b=Ctip2
markMSN3 = c('Ppp1r1b','Bcl11b','2010300C02Rik','Pde1b','Foxp1','Six3' )
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN3, embedding = "UMAP") #, imputeWeights = NULL)
p3 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p3))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f369a0933-Date-2021-01-22_Time-09-39-40.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-01-22 09:39:40 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f369a0933-Date-2021-01-22_Time-09-39-40.log
markMSN1 = c('Drd1','Tac1','Foxp2','Slc35d3','Chrm4', 'Pdyn') # D1 markers
# D1 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN1, embedding = "UMAP") #, imputeWeights = NULL) #
p1 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) +
theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p1))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f6bb5d615-Date-2021-01-22_Time-09-40-34.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-01-22 09:40:34 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f6bb5d615-Date-2021-01-22_Time-09-40-34.log
markMSN2 = c('Drd2','Adora2a','Penk', 'Grik3', 'Sp9', 'Gpr52')# D2 markers
# D2 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN2, embedding = "UMAP") #, imputeWeights = NULL)
p2 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p2))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f22cf94a2-Date-2021-01-22_Time-09-41-00.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-01-22 09:41:01 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f22cf94a2-Date-2021-01-22_Time-09-41-00.log
## Neuron vs. Glia markers
markerGenes1 <- c('Rbfox3', # Neuron
'Lhx6', #Interneuron
'Aqp4', # Astrocyte
'Cx3cr1', # Microglia
'Pdgfra', #OPC
'Mog' # Oligo
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAP") #, imputeWeights = NULL)
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f43bde249-Date-2021-01-22_Time-09-41-28.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-01-22 09:41:29 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f43bde249-Date-2021-01-22_Time-09-41-28.log
## plot more interneuron markers
markerGenes1 <- c('Lhx6', "Pvalb", 'Sst', 'Chat','Th', 'Vip') # Interneuron markers
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAP") #, imputeWeights = NULL)
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f443b403e-Date-2021-01-22_Time-09-49-36.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-01-22 09:49:37 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f443b403e-Date-2021-01-22_Time-09-49-36.log
############################################
# using marker gene scores, give cluster names
remapClust <- c(
'CNUGA' = 'Drop',
'CTGL' = 'Drop',
'CA3GL' = 'Drop',
'CLAGL' = 'Drop',
'DGNBL' = 'Drop',
'IOL' = 'Drop',
'ITL6GL' = 'Drop',
'L6bGL' = 'Drop',
'LSXGA' = 'Drop',
'PIRGL'= 'Drop',
'PTGL' = 'Drop',
'OBDOP' = 'Drop',
'OBGA1' = 'Drop',
# 'OBGL' = 'Drop',
'OBNBL' = 'Drop',
'OLFGL' = 'Drop',
'VPIA'= 'Drop',
'MSGA' = 'Drop',
'PER' = 'Drop',
'VEC' = 'Drop',
'VLMC' = 'Drop',
'SSTGA' = 'Drop',
'VIPGA' = 'Drop',
'LAMGA'= 'Drop',
'RGL' = 'Drop',
'STRGA' = 'Drop',
'D1MSN' = 'MSN_D1',
'D2MSN' = 'MSN_D2',
'MXD' = 'MSN_SN',
'PVGA' = 'INT_Pvalb',
'ASC' = 'Astro',
'OPC' = 'OPC',
'OGC' = 'Oligo',
'MGL' = 'Microglia')
proj$Clusters2 <- mapLabels(proj$L2cluster, newLabels = remapClust,
oldLabels = names(remapClust))
table(proj$Clusters2)
Astro Drop INT_Pvalb Microglia MSN_D1 MSN_D2 MSN_SN Oligo
1648 4287 268 645 6974 9466 637 2453
OPC
505
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Clusters2", embedding = "UMAP")
p1
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1f5f8d74883-Date-2021-01-22_Time-09-51-12.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1f5f8d74883-Date-2021-01-22_Time-09-51-12.log
# drop the drop clusters
ARCHDIR2=file.path(PROJDIR,'ArchR_BICCN_CP_labeled')
idxSample <- BiocGenerics::which(proj$Clusters2 %ni% "Drop")
cellsSample <- proj$cellNames[idxSample]
proj2 = subsetArchRProject(
ArchRProj = proj,
cells = cellsSample,
outputDirectory = ARCHDIR2, force =T
)
Dropping ImputeWeights Since You Are Subsetting Cells! ImputeWeights is a cell-x-cell Matrix!
Copying ArchRProject to new outputDirectory : /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/raw_data/mm10/BICCN_mouse_caudoputamen/ArchR_BICCN_CP_labeled
Copying Arrow Files...
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 2): Embeddings
Copying Other Files (2 of 2): IterativeLSI
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# make group coverage, call peaks, and
proj2<-addGroupCoverages(proj2, groupBy="Clusters2", force = TRUE)
proj2 = saveArchRProject(ArchRProj = proj2)
ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-1f5f3e9d752-Date-2021-01-22_Time-09-57-44.log
If there is an issue, please report to github with logFile!
Astro (1 of 8) : CellGroups N = 4
INT_Pvalb (2 of 8) : CellGroups N = 4
Microglia (3 of 8) : CellGroups N = 4
MSN_D1 (4 of 8) : CellGroups N = 4
MSN_D2 (5 of 8) : CellGroups N = 4
MSN_SN (6 of 8) : CellGroups N = 2
Oligo (7 of 8) : CellGroups N = 4
OPC (8 of 8) : CellGroups N = 4
2021-01-22 09:57:46 : Creating Coverage Files!, 0.033 mins elapsed.
2021-01-22 09:57:46 : Batch Execution w/ safelapply!, 0.033 mins elapsed.
2021-01-22 10:07:26 : Adding Kmer Bias to Coverage Files!, 9.699 mins elapsed.
Completed Kmer Bias Calculation
Adding Kmer Bias (1 of 30)
Adding Kmer Bias (2 of 30)
Adding Kmer Bias (3 of 30)
Adding Kmer Bias (4 of 30)
Adding Kmer Bias (5 of 30)
Adding Kmer Bias (6 of 30)
Adding Kmer Bias (7 of 30)
Adding Kmer Bias (8 of 30)
Adding Kmer Bias (9 of 30)
Adding Kmer Bias (10 of 30)
Adding Kmer Bias (11 of 30)
Adding Kmer Bias (12 of 30)
Adding Kmer Bias (13 of 30)
Adding Kmer Bias (14 of 30)
Adding Kmer Bias (15 of 30)
Adding Kmer Bias (16 of 30)
Adding Kmer Bias (17 of 30)
Adding Kmer Bias (18 of 30)
Adding Kmer Bias (19 of 30)
Adding Kmer Bias (20 of 30)
Adding Kmer Bias (21 of 30)
Adding Kmer Bias (22 of 30)
Adding Kmer Bias (23 of 30)
Adding Kmer Bias (24 of 30)
Adding Kmer Bias (25 of 30)
Adding Kmer Bias (26 of 30)
Adding Kmer Bias (27 of 30)
Adding Kmer Bias (28 of 30)
Adding Kmer Bias (29 of 30)
Adding Kmer Bias (30 of 30)
2021-01-22 10:17:35 : Finished Creation of Coverage Files!, 19.837 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addGroupCoverages-1f5f3e9d752-Date-2021-01-22_Time-09-57-44.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# call peaks
proj2<-addReproduciblePeakSet(proj2, groupBy = "Clusters2", plot = FALSE)
proj2 = saveArchRProject(ArchRProj = proj2)
Searching For MACS2.. Found with $path! ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-1f5f7e67acac-Date-2021-01-22_Time-10-17-48.log If there is an issue, please report to github with logFile! Calling Peaks with Macs2 2021-01-22 10:17:48 : Peak Calling Parameters!, 0.005 mins elapsed.
Group nCells nCellsUsed nReplicates nMin nMax maxPeaks Astro Astro 1648 1595 4 312 500 150000 INT_Pvalb INT_Pvalb 268 268 4 58 77 134000 Microglia Microglia 645 645 4 101 250 150000 MSN_D1 MSN_D1 6974 2000 4 500 500 150000 MSN_D2 MSN_D2 9466 1468 4 223 500 150000 MSN_SN MSN_SN 637 637 2 316 321 150000 Oligo Oligo 2453 1830 4 399 500 150000 OPC OPC 505 505 4 92 143 150000
2021-01-22 10:17:48 : Batching Peak Calls!, 0.005 mins elapsed.
2021-01-22 10:17:48 : Batch Execution w/ safelapply!, 0 mins elapsed.
2021-01-22 10:48:34 : Identifying Reproducible Peaks!, 30.772 mins elapsed.
2021-01-22 10:49:39 : Creating Union Peak Set!, 31.859 mins elapsed.
Converged after 5 iterations!
2021-01-22 10:49:45 : Finished Creating Union Peak Set (224763)!, 31.96 mins elapsed.
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# add peak counts matrix
proj2 <- addPeakMatrix(proj2)
proj2 = saveArchRProject(ArchRProj = proj2)
ArchR logging to : ArchRLogs/ArchR-addPeakMatrix-1f5f2f1905b6-Date-2021-01-22_Time-10-50-00.log
If there is an issue, please report to github with logFile!
2021-01-22 10:50:00 : Batch Execution w/ safelapply!, 0 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addPeakMatrix-1f5f2f1905b6-Date-2021-01-22_Time-10-50-00.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# add motif enrichment matrix
proj2 <- addMotifAnnotations(ArchRProj = proj2, motifSet = "cisbp", name = "Motif")
proj2 = saveArchRProject(ArchRProj = proj2)
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’
ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-1f5f5d7f649a-Date-2021-01-22_Time-10-53-44.log
If there is an issue, please report to github with logFile!
2021-01-22 10:53:50 : Gettting Motif Set, Species : Mus musculus, 0.004 mins elapsed.
Using version 2 motifs!
2021-01-22 10:53:53 : Finding Motif Positions with motifmatchr!, 0.058 mins elapsed.
2021-01-22 10:58:14 : Creating Motif Overlap Matrix, 4.41 mins elapsed.
2021-01-22 10:58:20 : Finished Getting Motif Info!, 4.501 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addMotifAnnotations-1f5f5d7f649a-Date-2021-01-22_Time-10-53-44.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# add motif deviations matrix
proj2 <- addBgdPeaks(proj2)
proj2 <- addDeviationsMatrix(proj2, peakAnnotation = "Motif", force = TRUE)
proj2 = saveArchRProject(ArchRProj = proj2)
Identifying Background Peaks! Using Previous Background Peaks! ArchR logging to : ArchRLogs/ArchR-addDeviationsMatrix-1f5f6c0bd04f-Date-2021-01-22_Time-10-59-11.log If there is an issue, please report to github with logFile!
NULL
2021-01-22 10:59:17 : Batch Execution w/ safelapply!, 0 mins elapsed.
###########
2021-01-22 12:12:28 : Completed Computing Deviations!, 73.283 mins elapsed.
###########
ArchR logging successful to : ArchRLogs/ArchR-addDeviationsMatrix-1f5f6c0bd04f-Date-2021-01-22_Time-10-59-11.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# add co-accessibility matrix
proj2 <- addCoAccessibility(proj2, reducedDims = "Harmony", dimsToUse = 1:30,
scaleDims = TRUE, corCutOff = 0.75, k = 100,
knnIteration = 500, overlapCutoff = 0.8,
maxDist = 1e+05, scaleTo = 10^4, log2Norm = TRUE)
ArchR logging to : ArchRLogs/ArchR-addCoAccessibility-1f5f1e1b1c02-Date-2021-01-22_Time-12-12-44.log If there is an issue, please report to github with logFile! 2021-01-22 12:12:44 : Computing KNN, 0.006 mins elapsed. 2021-01-22 12:12:44 : Identifying Non-Overlapping KNN pairs, 0.013 mins elapsed. 2021-01-22 12:12:47 : Identified 495 Groupings!, 0.061 mins elapsed. 2021-01-22 12:12:55 : Computing Co-Accessibility chr1 (1 of 20), 0.192 mins elapsed. 2021-01-22 12:13:05 : Computing Co-Accessibility chr2 (2 of 20), 0.361 mins elapsed. 2021-01-22 12:13:14 : Computing Co-Accessibility chr3 (3 of 20), 0.512 mins elapsed. 2021-01-22 12:13:23 : Computing Co-Accessibility chr4 (4 of 20), 0.655 mins elapsed. 2021-01-22 12:13:31 : Computing Co-Accessibility chr5 (5 of 20), 0.79 mins elapsed. 2021-01-22 12:13:39 : Computing Co-Accessibility chr6 (6 of 20), 0.929 mins elapsed. 2021-01-22 12:13:48 : Computing Co-Accessibility chr7 (7 of 20), 1.071 mins elapsed. 2021-01-22 12:13:55 : Computing Co-Accessibility chr8 (8 of 20), 1.191 mins elapsed. 2021-01-22 12:14:03 : Computing Co-Accessibility chr9 (9 of 20), 1.319 mins elapsed. 2021-01-22 12:14:10 : Computing Co-Accessibility chr10 (10 of 20), 1.445 mins elapsed. 2021-01-22 12:14:18 : Computing Co-Accessibility chr11 (11 of 20), 1.578 mins elapsed. 2021-01-22 12:14:27 : Computing Co-Accessibility chr12 (12 of 20), 1.726 mins elapsed. 2021-01-22 12:14:36 : Computing Co-Accessibility chr13 (13 of 20), 1.864 mins elapsed. 2021-01-22 12:14:43 : Computing Co-Accessibility chr14 (14 of 20), 1.988 mins elapsed. 2021-01-22 12:14:50 : Computing Co-Accessibility chr15 (15 of 20), 2.107 mins elapsed. 2021-01-22 12:14:57 : Computing Co-Accessibility chr16 (16 of 20), 2.224 mins elapsed. 2021-01-22 12:15:03 : Computing Co-Accessibility chr17 (17 of 20), 2.329 mins elapsed. 2021-01-22 12:15:10 : Computing Co-Accessibility chr18 (18 of 20), 2.431 mins elapsed. 2021-01-22 12:15:16 : Computing Co-Accessibility chr19 (19 of 20), 2.541 mins elapsed. 2021-01-22 12:15:21 : Computing Co-Accessibility chrX (20 of 20), 2.625 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-addCoAccessibility-1f5f1e1b1c02-Date-2021-01-22_Time-12-12-44.log
proj2 = saveArchRProject(ArchRProj = proj2)
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
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